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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Check clinical filter performance on clinical-db stage #2033

Closed northwestwitch closed 4 years ago

northwestwitch commented 4 years ago

Clinical filter of release 4.19, 4.20 and current master doesn't work any more. (Well, it returns no variants, but if one clicks on "filter" immediately after, it works).

Thankfully (🙏) everything works on prod (version 4.19)

northwestwitch commented 4 years ago

I'll try to figure out this one now!

northwestwitch commented 4 years ago

Comparison at the query level when you first push the clinical filter button (doesn't work):

{'case_id': 'strongbison', 'category': 'snv', 'variant_type': 'clinical', 'panels': {'$in': ['OMIM-AUTO']}, 'chromosome': 'None', '$or': [{'$and': [{'$or': [{'gnomad_frequency': {'$lt': 0.01}}, {'gnomad_frequency': {'$exists': False}}]}, {'genes.functional_annotation': {'$in': ['transcript_ablation', 'splice_donor_variant', 'splice_acceptor_variant', 'stop_gained', 'frameshift_variant', 'stop_lost', 'start_lost', 'initiator_codon_variant', 'inframe_insertion', 'inframe_deletion', 'missense_variant', 'protein_altering_variant', 'transcript_amplification', 'splice_region_variant', 'incomplete_terminal_codon_variant', 'synonymous_variant', 'start_retained_variant', 'stop_retained_variant', 'coding_sequence_variant']}}, {'genes.region_annotation': {'$in': ['exonic', 'splicing']}}]}, {'clnsig': {'$elemMatch': {'$and': [{'$or': [{'value': {'$in': [4, 'Likely pathogenic', 5, 'Pathogenic']}}, {'value': re.compile('Likely pathogenic|Pathogenic')}]}, {'revstat': re.compile('mult|multiple_submitters|single|single_submitter|exp|reviewed_by_expert_panel|guideline|practice_guideline')}]}}}]}

And when you click on filter variants immediately after (works): {'case_id': 'strongbison', 'category': 'snv', 'variant_type': 'clinical', 'panels': {'$in': ['OMIM-AUTO']}, '$or': [{'$and': [{'$or': [{'gnomad_frequency': {'$lt': 0.01}}, {'gnomad_frequency': {'$exists': False}}]}, {'genes.functional_annotation': {'$in': ['transcript_ablation', 'splice_donor_variant', 'splice_acceptor_variant', 'stop_gained', 'frameshift_variant', 'stop_lost', 'start_lost', 'initiator_codon_variant', 'inframe_insertion', 'inframe_deletion', 'missense_variant', 'protein_altering_variant', 'transcript_amplification', 'splice_region_variant', 'incomplete_terminal_codon_variant', 'synonymous_variant', 'start_retained_variant', 'stop_retained_variant', 'coding_sequence_variant']}}, {'genes.region_annotation': {'$in': ['exonic', 'splicing']}}]}, {'clnsig': {'$elemMatch': {'$and': [{'$or': [{'value': {'$in': [4, 'Likely pathogenic', 5, 'Pathogenic']}}, {'value': re.compile('Likely pathogenic|Pathogenic')}]}, {'revstat': re.compile('mult|multiple_submitters|single|single_submitter|exp|reviewed_by_expert_panel|guideline|practice_guideline')}]}}}]}

The first one has an extra key/value : 'chromosome': 'None'. Found the bug!